fixed more fails

broadinstitute · Dec 22, 2023 · 78260d1 · 78260d1
1 parent e6f806f
commit 78260d1
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/src/main/java/picard/cmdline/CommandLineProgram.java b/src/main/java/picard/cmdline/CommandLineProgram.java
@@ -344,7 +344,7 @@ protected boolean parseArgs(final String[] argv) {
         final PicardHtsPath picardHtsPath = referenceSequence.getHtsPath();
         REFERENCE_SEQUENCE = picardHtsPath == null ?
                 null :
-                new File(picardHtsPath.getRawInputString());
+                new File(picardHtsPath.getURI().getPath()); // Must remove the "file://" prefix
 
         // The TMP_DIR setting section below was moved from instanceMain() to here due to timing issues
         // related to checking whether R is installed. Certain programs, such as CollectInsertSizeMetrics

diff --git a/src/main/java/picard/nio/PicardBucketUtils.java b/src/main/java/picard/nio/PicardBucketUtils.java
@@ -67,6 +67,7 @@ public static PicardHtsPath getTempFilePath(final String directory, String prefi
         }
     }
 
+    // For local temp file, directory should be null.
     public static PicardHtsPath getTempFilePath(String directory, String extension){
         return getTempFilePath(directory, "", extension);
     }

diff --git a/src/test/java/picard/util/IntervalListToolsTest.java b/src/test/java/picard/util/IntervalListToolsTest.java
@@ -263,8 +263,9 @@ private long testerCountOutput(IntervalListTools.Action action, IntervalListTool
     private long testerCountOutput(IntervalListTools.Action action, IntervalListTools.Output outputValue, boolean invert,
                                    boolean unique, boolean dontMergeAbutting, Path input1, Path input2,
                                    final boolean cloudOutput) throws IOException {
-        final String outputDirFullName = cloudOutput ? CLOUD_OUTPUT_DIR : "IntervalListTools";
-        final PicardHtsPath countOutput = PicardBucketUtils.getTempFilePath(outputDirFullName, ".txt");
+        final String outputDirFullName = cloudOutput ? CLOUD_OUTPUT_DIR : null;
+        final String prefix = "IntervalListTools";
+        final PicardHtsPath countOutput = PicardBucketUtils.getTempFilePath(outputDirFullName, prefix, ".txt");
 
         final List<String> args = buildStandardTesterArguments(action, invert, unique, dontMergeAbutting, input1, input2);
         args.add("OUTPUT_VALUE=" + outputValue);